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SLX1A SLX1 homolog A, structure-specific endonuclease subunit [ Homo sapiens (human) ]

Gene ID: 548593, updated on 5-Mar-2024

Summary

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Official Symbol
SLX1Aprovided by HGNC
Official Full Name
SLX1 homolog A, structure-specific endonuclease subunitprovided by HGNC
Primary source
HGNC:HGNC:20922
See related
Ensembl:ENSG00000132207 MIM:615822; AllianceGenome:HGNC:20922
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
GIYD1
Summary
This gene encodes a protein that is an important regulator of genome stability. The protein represents the catalytic subunit of the SLX1-SLX4 structure-specific endonuclease, which can resolve DNA secondary structures that are formed during repair and recombination processes. Two identical copies of this gene are located on the p arm of chromosome 16 due to a segmental duplication; this record represents the more centromeric copy. Alternative splicing results in multiple transcript variants. Read-through transcription also occurs between this gene and the downstream SULT1A3 (sulfotransferase family, cytosolic, 1A, phenol-preferring, member 3) gene. [provided by RefSeq, Nov 2010]
Expression
Ubiquitous expression in duodenum (RPKM 34.0), small intestine (RPKM 29.1) and 24 other tissues See more
Orthologs
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Genomic context

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Location:
16p11.2
Exon count:
6
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (30193843..30197566)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (30478393..30482118)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (30205164..30208887)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7358 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:30195204-30195744 Neighboring gene CORO1A antisense RNA 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:30195745-30196286 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:30196287-30196826 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:30196827-30197368 Neighboring gene coronin 1A Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10695 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:30197909-30198449 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:30198450-30198989 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr16:30204716-30205440 Neighboring gene SLX1A-SULT1A3 readthrough (NMD candidate) Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:30206166-30206889 Neighboring gene bolA family member 2B Neighboring gene sulfotransferase family 1A member 3 Neighboring gene SAGA complex associated factor 29 pseudogene

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. Folate stress induces SLX1- and RAD51-dependent mitotic DNA synthesis at the fragile X locus in human cells. Garribba L, et al. Proc Natl Acad Sci U S A, 2020 Jul 14. PMID 32601218, Free PMC Article
  2. Coordinated actions of SLX1-SLX4 and MUS81-EME1 for Holliday junction resolution in human cells. Wyatt HD, et al. Mol Cell, 2013 Oct 24. PMID 24076221
  3. Regulation of multiple DNA repair pathways by the Fanconi anemia protein SLX4. Kim Y, et al. Blood, 2013 Jan 3. PMID 23093618, Free PMC Article
  4. Human SULT1A3 pharmacogenetics: gene duplication and functional genomic studies. Hildebrandt MA, et al. Biochem Biophys Res Commun, 2004 Sep 3. PMID 15358107
  5. SLX4-SLX1 Protein-independent Down-regulation of MUS81-EME1 Protein by HIV-1 Viral Protein R (Vpr). Zhou X, et al. J Biol Chem, 2016 Aug 12. PMID 27354282, Free PMC Article

See all (20) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Folate stress induces SLX1- and RAD51-dependent mitotic DNA synthesis at the fragile X locus in human cells.
    Title: Folate stress induces SLX1- and RAD51-dependent mitotic DNA synthesis at the fragile X locus in human cells.
  2. SLX4-SLX1 Protein-independent Down-regulation of MUS81-EME1 Protein by HIV-1 Viral Protein R (Vpr).
    Title: SLX4-SLX1 Protein-independent Down-regulation of MUS81-EME1 Protein by HIV-1 Viral Protein R (Vpr).
  3. Data show that three structure-selective endonucleases, SLX1-SLX4, MUS81-EME1, and GEN1, define two pathways of Holliday junctions (HJs) resolution in HeLa cells.
    Title: Coordinated actions of SLX1-SLX4 and MUS81-EME1 for Holliday junction resolution in human cells.
Submit: New GeneRIF Correction

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Readthrough SLX1A-SULT1A3

Readthrough gene: SLX1A-SULT1A3, Included gene: SULT1A3

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables 5'-flap endonuclease activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables 5'-flap endonuclease activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables crossover junction DNA endonuclease activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables crossover junction DNA endonuclease activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in DNA double-strand break processing involved in repair via single-strand annealing IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in DNA repair IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in double-strand break repair via homologous recombination IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in double-strand break repair via homologous recombination IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in negative regulation of telomere maintenance via telomere lengthening IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in positive regulation of t-circle formation ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in t-circle formation IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in t-circle formation ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in telomere maintenance via telomere lengthening IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in telomeric D-loop disassembly IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
part_of Slx1-Slx4 complex IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of Slx1-Slx4 complex IDA
Inferred from Direct Assay
more info
 PubMed 
part_of Slx1-Slx4 complex TAS
Traceable Author Statement
more info
 PubMed 
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
  
located_in nucleoplasm TAS
Traceable Author Statement
more info
  

General protein information

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Preferred Names
structure-specific endonuclease subunit SLX1
Names
GIY-YIG domain-containing protein 1
SLX1 structure-specific endonuclease subunit homolog A

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_001014999.3 → NP_001014999.1  structure-specific endonuclease subunit SLX1 isoform 1

    See identical proteins and their annotated locations for NP_001014999.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
    Source sequence(s)
    AI885276, BC144462, BI757439, CD673028
    Consensus CDS
    CCDS32431.1
    UniProtKB/Swiss-Prot
    B7ZME1, Q6NTG6, Q9BQ83
    UniProtKB/TrEMBL
    Q9H5H2
    Related
    ENSP00000251303.7, ENST00000251303.11
    Conserved Domains (1) summary
    cd10455
    Location:13 → 89
    GIY-YIG_SLX1; Catalytic GIY-YIG domain of yeast structure-specific endonuclease subunit SLX1 and its eukaryotic homologs

  2. NM_001015000.2 → NP_001015000.1  structure-specific endonuclease subunit SLX1 isoform 2

    See identical proteins and their annotated locations for NP_001015000.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an alternate in-frame exon in the central coding region, compared to variant 1, resulting in an isoform (2) that is shorter than isoform 1.
    Source sequence(s)
    AI885276, BC144462, BI757439
    Consensus CDS
    CCDS32432.1
    UniProtKB/Swiss-Prot
    Q9BQ83
    Related
    ENSP00000333945.4, ENST00000345535.8
    Conserved Domains (1) summary
    cd10455
    Location:13 → 82
    GIY-YIG_SLX1; Catalytic GIY-YIG domain of yeast structure-specific endonuclease subunit SLX1 and its eukaryotic homologs

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000016.10 Reference GRCh38.p14 Primary Assembly

    Range
    30193843..30197566
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060940.1 Alternate T2T-CHM13v2.0

    Range
    30478393..30482118
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9BQ83.1 GenPept UniProtKB/Swiss-Prot:Q9BQ83

Gene LinkOut

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